My problem is that Moho doesn't know how to tell which shape should be in front of another. I've tried using just the layer order. I've tried using "Sort by True Distance" in the Project Properties. But Moho keeps getting tripped up.

See for yourself:

As you can see the red wall keeps getting confused with the floor & ceiling. Also the ladder rails I set up keep vanishing behind the tan wall.

Just to throw my thoughts in here (and there are a number of much older posts which discuss this), if you are sorting by "depth", you really need to be careful where the layers origin is placed. In layer depth sorting, Moho doesn't really consider whats in the layer, only the relative depths of the origins of the various layers. Sometimes you have to play some tricks for particular angles. If for example, you have a side wall that ends up with it's origin somewhere near the far end of the wall, you may not have to rotate the scene very far before Moho suddenly thinks the back wall is closer to the camera, and everything goes haywire.